Contacts of the helix formed by residues 396 - 412 (chain B) in PDB entry 1B3U
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 396 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B ASN* 3.8 31.3 + - - +
394B ILE 3.7 1.4 + - - -
395B GLY* 1.3 71.4 - - - -
397B ARG* 1.3 67.1 + - + +
399B LEU* 3.8 5.3 - - + +
400B SER* 3.1 35.2 + - - +
433B LEU* 4.2 25.8 - - + +
436B GLU* 4.6 30.5 - - + +
437B PHE* 4.4 10.1 - - + -
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Residues in contact with ARG 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LYS* 5.4 4.8 - - - +
395B GLY* 4.2 11.0 - - - -
396B ILE* 1.3 85.9 - - + +
398B GLN* 1.3 95.5 + - - +
400B SER* 4.3 4.6 - - - -
401B GLN* 3.5 38.6 + - - +
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Residues in contact with GLN 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LYS* 4.5 13.2 - - - -
361B ILE* 3.7 26.9 - - + +
365B LEU* 4.8 7.4 - - + +
394B ILE* 4.2 14.3 - - + +
395B GLY* 2.7 25.9 + - - +
397B ARG* 1.3 104.3 - - - +
399B LEU* 1.3 63.4 + - - +
401B GLN* 3.5 36.8 + - - +
402B SER* 4.0 7.3 + - - -
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 5.2 3.6 - - + -
368B PHE* 4.6 19.3 - - + -
387B LEU* 4.9 10.1 - - + +
390B VAL* 4.7 9.4 - - + -
391B ASN* 3.6 40.2 - - + +
394B ILE* 4.1 17.4 - - + +
395B GLY 3.1 9.0 + - - +
396B ILE* 3.8 9.9 - - + +
397B ARG 3.3 0.2 - - - -
398B GLN* 1.3 74.6 - - - +
400B SER* 1.3 67.1 + - - +
401B GLN 3.0 1.3 - - - -
402B SER* 2.9 12.2 + - - +
403B LEU* 2.9 39.5 + - + +
433B LEU* 3.9 18.6 - - + -
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Residues in contact with SER 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ILE* 3.1 19.8 + - - +
397B ARG* 4.3 5.2 - - - -
399B LEU* 1.3 77.0 - - - +
401B GLN* 1.3 64.7 + - - +
403B LEU* 4.3 3.6 - - - -
404B LEU* 2.9 43.6 + - - +
405B PRO* 3.4 0.3 - - - +
436B GLU 5.3 0.9 + - - -
437B PHE* 3.2 35.1 + - - -
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Residues in contact with GLN 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ARG* 3.5 24.1 + - - +
398B GLN* 3.5 39.9 + - - +
399B LEU 3.0 0.2 + - - -
400B SER* 1.3 80.2 - - - +
402B SER* 1.3 57.7 + - - +
405B PRO* 3.3 17.7 - - - +
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Residues in contact with SER 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 3.9 30.6 - - - +
368B PHE* 5.1 2.1 - - - -
369B LEU* 3.5 37.6 - - - +
398B GLN 4.0 3.6 + - - -
399B LEU* 2.9 13.8 + - - +
401B GLN* 1.3 77.2 - - - +
403B LEU* 1.3 65.5 + - - +
405B PRO* 3.5 9.5 - - - +
406B ALA* 4.0 6.1 + - - +
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B PHE* 4.4 13.0 - - + -
372B LEU* 3.5 28.3 - - + -
384B ILE* 4.4 8.3 - - + -
387B LEU* 4.6 7.9 - - + -
399B LEU* 2.9 32.2 + - + +
400B SER* 4.3 1.1 - - - -
402B SER* 1.3 77.2 + - - +
404B LEU* 1.3 69.0 + - - +
406B ALA* 2.9 18.8 + - - +
407B ILE* 3.0 31.1 + - + -
429B LEU* 4.3 8.7 - - + -
433B LEU* 4.0 17.3 - - + -
437B PHE* 3.8 22.9 - - + -
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B SER* 2.9 29.3 + - - +
403B LEU* 1.3 76.4 - - - +
405B PRO* 1.3 54.2 - - + +
407B ILE* 3.2 9.3 + - + +
408B VAL* 2.7 53.6 + - + +
437B PHE* 4.8 10.3 - - + -
439B ASP* 3.6 24.5 - - - +
441B LYS* 4.0 18.8 - - + -
442B LEU* 3.7 38.6 - - + -
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Residues in contact with PRO 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LYS* 5.7 0.2 - - - +
400B SER 3.4 9.6 - - - +
401B GLN 3.3 19.5 - - - +
402B SER* 3.5 7.0 - - - +
403B LEU 3.2 4.7 - - - -
404B LEU* 1.3 96.2 - - + +
406B ALA* 1.3 56.4 + - - +
408B VAL* 3.2 8.2 + - + +
409B GLU* 2.9 38.1 + - - +
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Residues in contact with ALA 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU* 4.7 2.9 - - + -
372B LEU* 3.6 28.0 - - + -
373B LYS* 3.2 37.4 + - + +
402B SER 4.0 7.9 + - - +
403B LEU 2.9 11.5 + - - +
405B PRO* 1.3 75.3 - - - +
407B ILE* 1.3 66.2 + - - +
409B GLU* 3.3 5.3 + - - +
410B LEU* 3.2 24.0 + - + +
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Residues in contact with ILE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 5.3 2.2 - - + -
384B ILE* 5.3 4.9 - - + -
403B LEU* 3.0 42.6 + - + +
404B LEU* 3.3 10.5 - - + +
406B ALA* 1.3 72.9 - - - +
408B VAL* 1.3 71.3 + - - +
410B LEU* 2.7 21.4 + - - +
411B ALA* 2.8 10.6 + - + -
422B ILE* 4.3 25.6 - - + -
425B TYR* 6.3 1.1 - - + -
426B MET* 5.1 3.1 - - + -
429B LEU* 3.4 33.7 - - + -
437B PHE* 4.1 9.9 - - + -
442B LEU* 4.8 9.6 - - + -
445B LEU* 4.5 13.0 - - + -
449B TRP* 5.7 0.4 - - + -
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Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LEU* 2.7 30.6 + - + +
405B PRO* 3.3 12.1 - - + +
407B ILE* 1.3 71.3 - - - +
409B GLU* 1.3 63.0 + - + +
411B ALA* 3.1 15.2 + - - +
412B GLU* 2.6 34.6 - - - +
441B LYS* 3.8 38.4 - - + +
445B LEU* 3.6 28.0 - - + -
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Residues in contact with GLU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LYS* 2.7 33.7 + - - +
405B PRO* 2.9 21.1 + - - +
406B ALA* 3.3 7.7 - - - +
407B ILE 2.8 0.8 + - - -
408B VAL* 1.3 81.2 - - + +
410B LEU* 1.3 64.4 + - + +
412B GLU* 3.3 26.0 + - - +
413B ASP* 3.9 4.5 + - - +
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B LEU* 4.3 13.5 - - + +
373B LYS* 5.4 11.0 - - + -
380B ARG* 3.6 34.3 - - + +
406B ALA* 3.5 14.4 - - + +
407B ILE* 2.7 10.9 + - - +
409B GLU* 1.3 75.8 - - + +
411B ALA* 1.3 63.7 + - - +
412B GLU 3.0 3.1 + - - -
413B ASP* 3.3 25.9 + - - +
418B VAL* 4.1 16.2 - - + +
419B ARG* 4.1 4.0 - - - +
422B ILE* 3.3 40.8 - - + +
425B TYR* 5.3 0.2 - - + -
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Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ILE 2.8 9.5 + - - +
408B VAL 3.1 11.4 + - - +
410B LEU* 1.3 77.4 - - - +
412B GLU* 1.3 58.2 + - - +
413B ASP 3.5 0.2 - - - -
419B ARG* 3.5 13.8 - - - +
422B ILE* 4.0 6.7 - - + +
445B LEU* 3.9 28.5 - - + -
449B TRP* 3.4 46.9 + - + +
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Residues in contact with GLU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B VAL* 2.6 41.1 - - - +
409B GLU* 3.4 15.4 - - - +
410B LEU 3.0 0.2 - - - -
411B ALA* 1.3 78.7 - - + +
413B ASP* 1.3 61.0 + - - +
414B ALA 3.8 1.6 + - - -
419B ARG* 4.4 4.0 - - - +
441B LYS* 5.4 2.8 + - - -
445B LEU* 5.5 5.9 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il